Man pages for Bioconductor-mirror/ScISI
In Silico Interactome

arp23Constituent members of Protein Complex Arp 2/3
arp23GThe graph of arg 2/3
arp23OrfConstituent members of Protein Complex Arp 2/3
arp23Y2HGA graph of ARP 2/3 containing only Y2H verified interactions
calcGraphStatsA function to calculate the various summary statistics for...
cfiaConstituent members of Protein Complex Cleavage Factor IA...
cfiaOrfConstituent members of Protein Complex Cleavage Factor IA...
checkComplexFunction to check a list of protein complexes wrt ScISI
checkSGNA function to check that the protein names are all systematic...
compareComplexA function to compare two bipartite graph matrices
compBijectionA recursive function that greedily handles the alignment...
createGODataFrameA function to create a Dataframe from the GO protein...
createGOMatrixA function to create the bipartite graph (BG) incidence...
createMipsDataFrameA function that creates a data frame from the MIPS Data
createMipsMatrixA function to create the bipartite graph incidence matrix...
createYeastDataObjCreates an object of class yeastData
dataSA character matrix containing the source data for the ScISI
Desc-methodsA method to return a description of a protein complex
eAtAn edge attribute data file
eAt2A file containing edge attributes
edgePropA function to estimate the edge proportion of a y2h induced...
egEBI16112A graph example mapping an IntAct ID to Systematic Gene Names
expStatsA data file containing the experimental statistics
findSubCompA function that looks for either equality between two...
gavin2mergeMGA data file containing the pre-merged Gavin to (merged)...
getAPMSDataA function to get the estimated complexes from high...
getGOInfoA function that parses through the GO database; it agreps for...
getLocOrfsA function to obtain ORFs for the ScISI
getMipsInfoA function that reads the downloaded text file from the MIPS...
getURL-methodsA method to return an url location of a protein complex
graphSumStatsAn initiation function to generate graph statistics
ho2mergeMGGA data file containing the pre-merged Ho to the (merged)...
ID-methodsA method to return the ID of a protein complex
JaccardCoefA function to calculate the Jaccard similarity index between...
krogan2mergeMGGHA data file containing the pre-merged Krogan to the (merged)...
locScISIA data file used to estimate the location of the complexes of...
mapping2SysGA example graph of the mapping from IntAct to Systematic...
mappingsGA example graph of the mapping from IntAct to Systematic...
maximizeSimilarityA function compares two bipartite graph matrices and finds...
meanDegA function to estimate the population mean nodal degree of a...
mergeBGMatA function that merges two bipartite graph (BG) incidence...
mips2goA data file containing the pre-merged GO to the MIPS data
nAtA file containing node attributes
nAtMapA file containing node attributes
nonGenesGenes found in MIPS which are not gene locus names
nucCompA data file containing the nuclear complexes
recCompSizeA function that records the relative sizes of complex C-i...
redundantMA matrix of redundant complex summary statistics
rmByEviA function that parses through each GO protein complex and...
runAlignmentA function to establish preliminaries for the compBijection...
runCompareComplexA function that calls all other types of comparison functions
ScISIThe In Silico Interactome for Saccharomyces cerevisiae
ScISI2htmlA function that generates an html page for the GO and MIPs...
subCompMA matrix of sub-complex summary statistics
sumStatsA function to calculate some summary statistics between an...
unwantedGO terms that are parsed but not protein complexes
unWantedCompA function to manually remove protein complexes from some in...
xtraGOA character vector of hand selected GO protein complexes
xtraGONodesA function to check manually curated GO nodes
yeastData-classClass "yeastData"
Bioconductor-mirror/ScISI documentation built on June 1, 2017, 2:18 a.m.